METHODS AND SYSTEMS FOR DETERMINING THE CELLULAR ORIGIN OF CELL-FREE DNA

Provided herein are methods for determining the cellular origin of cell-free DNA. In one aspect, the methods include constructing a distribution of sequence and/or epigenetic information from DNA molecules obtained from a cfDNA sample over a plurality of base positions of a set of differential genomic sections or loci that comprise genomic regions and/or epigenetic loci. The differential genomic loci exhibit one or more properties that differ between at least two cell types. The methods also include processing the distribution of the sequence and/or epigenetic information from the DNA molecules over the set of the differential genomic loci to determine the cellular origin of at least a subset of DNA molecules from the cfDNA sample. Other aspects are directed to methods of treating disease in subjects. Yet other aspects include related systems and computer readable media used to determine the cellular origin of cfDNA.